miRNAome analysis associated with anatomic and transcriptomic investigations reveal the polar exhibition of corky split vein in boron deficient Citrus sinensis

What Can Boron Deficiency Symptoms Tell Us about Its Function and Regulation?

On the eve of the 100th anniversary of Dr. Warington's discovery of boron (B) as a nutrient essential for higher plants, "boronists" have struggled to demonstrate a role beyond its structural function in cell walls dimerizing pectin molecules of rhamnogalacturonan II (RGII). In this regard, B deficiency has been associated with a plethora of symptoms in plants that include macroscopic symptoms like growth arrest and cell death and biochemical or molecular symptoms that include changes in cell wall pore size, apoplast acidification, or a steep ROS production that leads to an oxidative burst. Aiming to shed light on B functions in plant biology, we proposed here a unifying model integrating the current knowledge about B function(s) in plants to explain why B deficiency can cause such remarkable effects on plant growth and development, impacting crop productivity. In addition, based on recent experimental evidence that suggests the existence of different B ligands other than RGII in plant cells, namely glycolipids, and glycoproteins, we proposed an experimental pipeline to identify putative missing ligands and to determine how they would integrate into the above-mentioned model.

The regulation of plant lignin biosynthesis under boron deficiency conditions

Boron (B) is a required micronutrient that is crucial for the growth and development of vascular plants. A deficiency in B is generally regarded as a limiting factor affecting agricultural production in many parts of the world. Boron is involved in the metabolism of plant lignin and additionally, B deficiency can lead to the excessive accumulation of lignin in plant leaves/roots, resulting in corking symptoms and inhibited growth. However, the effect of B on lignin biosynthesis is not as well characterized as the specific function of B in the cell wall. In this article, recent studies on the regulation of lignin biosynthesis in plants under low-B stress conditions are reviewed. Moreover, the following possible mechanisms underlying the lignin synthesis promoted by B deficiency are discussed: (1) the accumulation of phenolic substances during B deficiency directly enhances lignin synthesis; (2) excess H₂ O₂ has a dual function to the enhancement of lignin under boron deficiency conditions, serving as a substrate and a signaling molecule; and (3) B deficiency regulates lignin synthesis through the expression of genes encoding transcription factors such as MYBs. Finally, future studies regarding physiology, molecules, and transcriptional regulation may reveal the mechanism(s) mediating the relationship between lignin synthesis and B deficiency. This review provides new insights and important references for future research and the enhancement of plant B nutrition.

Identification and function prediction of iron-deficiency-responsive microRNAs in citrus leaves

Iron is a critical micronutrient for growth and development of plants and its deficiency limiting the crop productivity. MicroRNAs (miRNAs) play vital roles in adaptation of plants to various nutrient deficiencies. However, the role of miRNAs and their target genes related to Fe-deficiency is limited. In this study, we identified Fe-deficiency-responsive miRNAs from citrus. In Fe-deficiency conditions, about 50 and 31 miRNAs were up-regulated and down-regulated, respectively. The differently expressed miRNAs might play critical roles in contributing the Fe-deficiency tolerance in citrus plants. The miRNAs-mediated Fe-deficiency tolerance in citrus plants might related to the enhanced stress tolerance by decreased expression of miR172; regulation of S homeostasis by decreased expression of miR395; inhibition of plant growth by increased expression of miR319 and miR477; regulation of Cu homeostasis as well as activation of Cu/Zn superoxide dismutase activity due to decreased expression of miR398 and miR408 and regulation of lignin accumulation by decreased expression of miR397 and miR408. The identified miRNAs in present study laid a foundation to understand the Fe-deficiency adaptive mechanisms in citrus plants.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02669-z.

Molecular mechanisms for magnesium-deficiency-induced leaf vein lignification, enlargement and cracking in Citrus sinensis revealed by RNA-Seq

Citrus sinensis (L.) Osbeck seedlings were fertigated with nutrient solution containing 2 [magnesium (Mg)-sufficiency] or 0 mM (Mg-deficiency) Mg(NO3)2 for 16 weeks. Thereafter, RNA-Seq was used to investigate Mg-deficiency-responsive genes in the veins of upper and lower leaves in order to understand the molecular mechanisms for Mg-deficiency-induced vein lignification, enlargement and cracking, which appeared only in the lower leaves. In this study, 3065 upregulated and 1220 downregulated, and 1390 upregulated and 375 downregulated genes were identified in Mg-deficiency veins of lower leaves (MDVLL) vs Mg-sufficiency veins of lower leaves (MSVLL) and Mg-deficiency veins of upper leaves (MDVUL) vs Mg-sufficiency veins of upper leaves (MSVUL), respectively. There were 1473 common differentially expressed genes (DEGs) between MDVLL vs MSVLL and MDVUL vs MSVUL, 1463 of which displayed the same expression trend. Magnesium-deficiency-induced lignification, enlargement and cracking in veins of lower leaves might be related to the following factors: (i) numerous transciption factors and genes involved in lignin biosynthesis pathways, regulation of cell cycle and cell wall metabolism were upregulated; and (ii) reactive oxygen species, phytohormone and cell wall integrity signalings were activated. Conjoint analysis of proteome and transcriptome indicated that there were 287 and 56 common elements between DEGs and differentially abundant proteins (DAPs) identified in MDVLL vs MSVLL and MDVUL vs MSVUL, respectively, and that among these common elements, the abundances of 198 and 55 DAPs matched well with the transcript levels of the corresponding DEGs in MDVLL vs MSVLL and MDVUL vs MSVUL, respectively, indicating the existence of concordances between protein and transcript levels.

Modulation of disease severity by plant positive-strand RNA viruses: The complex interplay of multifunctional viral proteins, subviral RNAs and virus-associated RNAs with plant signaling pathways and defense responses

Plant viruses induce a range of symptoms of varying intensity, ranging from severe systemic necrosis to mild or asymptomatic infection. Several evolutionary constraints drive virus virulence, including the dependence of viruses on host factors to complete their infection cycle, the requirement to counteract or evade plant antiviral defense responses and the mode of virus transmission. Viruses have developed an array of strategies to modulate disease severity. Accumulating evidence has highlighted not only the multifunctional role that viral proteins play in disrupting or highjacking plant factors, hormone signaling pathways and intracellular organelles, but also the interaction networks between viral proteins, subviral RNAs and/or other viral-associated RNAs that regulate disease severity. This review focusses on positive-strand RNA viruses, which constitute the majority of characterized plant viruses. Using well-characterized viruses with different genome types as examples, recent advances are discussed as well as knowledge gaps and opportunities for further research.

Combined analysis of mRNA and miRNA identifies dehydration and salinity responsive key molecular players in citrus roots

Citrus is one of the most economically important fruit crops around world. Drought and salinity stresses adversely affected its productivity and fruit quality. However, the genetic regulatory networks and signaling pathways involved in drought and salinity remain to be elucidated. With RNA-seq and sRNA-seq, an integrative analysis of miRNA and mRNA expression profiling and their regulatory networks were conducted using citrus roots subjected to dehydration and salt treatment. Differentially expressed (DE) mRNA and miRNA profiles were obtained according to fold change analysis and the relationships between miRNAs and target mRNAs were found to be coherent and incoherent in the regulatory networks. GO enrichment analysis revealed that some crucial biological processes related to signal transduction (e.g. ‘MAPK cascade’), hormone-mediated signaling pathways (e.g. abscisic acid- activated signaling pathway’), reactive oxygen species (ROS) metabolic process (e.g. ‘hydrogen peroxide catabolic process’) and transcription factors (e.g., ‘MYB, ZFP and bZIP’) were involved in dehydration and/or salt treatment. The molecular players in response to dehydration and salt treatment were partially overlapping. Quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) analysis further confirmed the results from RNA-seq and sRNA-seq analysis. This study provides new insights into the molecular mechanisms how citrus roots respond to dehydration and salt treatment.